Genomes and Annotation: ElDorado

ElDorado is
the Genomatix genome annotation. It is based on the publicly available reference
genome assemblies of 33 different organisms.
Information from
a variety of different sources together with data generated by Genomatix’ proprietary
algorithms is used to set up a database of more than 500 gigabyte of quality
checked data. The individual elements are highly linked to external data sources
(e.g. NCBI, Ensembl, EntrezGene, ...).

Representing a common sequence basis it allows us to integrate literature
based information about gene-gene interactions and pathway annotation from
Genomatix Pathway System (GePS)
together
with experimental gene expression data.

Comparative
Genomics allows you
to compare the annotation available for a group of
orthologous genes and to identify corresponding promoter
regions for the analysis of phylogenetically conserved
promoter elements.

Literature analysis gives you access
to the genes cocited in the scientific literature
providing direct links to Genomatix Pathway System
(GePS) for
further in-depth analysis.

ElDorado allows to enter gene names, GeneIDs from EntrezGene and Emsembl, Affymetrix IDs, sequences, or regions on a genomic contig. In case the input is a sequence, this sequence is directly mapped to the genomes.

The gene names included in ElDorado are based on
EntrezGene.
The input may contain the following gene related keywords:

Gene symbols (e.g. HMGA1).

Full gene names (e.g. high mobility group AT-hook 1) or more
general expressions describing a complex group of genes
(e.g. transcription factor or G protein coupled receptor).
Wildcards (e.g. COX*) are also possible.

Accession numbers of transcripts that have been mapped to the
ElDorado genomes. These include accession numbers from RefSeq
(e.g. NM_002131) and Ensembl (e.g. ENST00000327014) as
well as full-length transcripts from GenBank (e.g. AK096863).

Genomatix Promoter Ids starting with "GXP_" like GXP_311812

SNP identifiers from dbSNP (e.g. rs11557697).

MicroRNA IDs from miRBase (e.g. mmu-mir-668 or
MI0004134).

Affymetrix probe set Ids (e.g. 210457_x_at).

Only Affymetrix probe set Ids from the default chips of the
organisms are searched. You can view and change the default chips on
the "Personal" page of your account.

The assignment of Affymetrix probe set identifiers to transcripts
is based on genomic mapping of each single probe. A transcript will
be displayed if at least one single oligo-nucleotide probe of the
probe set (usually 11 probes) matches. For mixed probe sets
(cross-hybridisation) all relevant transcripts are displayed.

Per default, all ElDorado database tables containing gene related keywords are searched in a defined order. To restrict your search to a certain keyword (e.g. Gene IDs or gene symbols), choose it from the list to the right of the text field.

These requests result in a list of genes corresponding to the submitted
expression. Each entry consists of a gene description, the gene symbol,
and the chromosome it is located on. The request can then be continued
by clicking on one of the provided links. In case the element
corresponding to the keyword entered is not located nearby a known gene
(e.g. rs7510768), only the genomic context is displayed in ElDorado.

You can also enter a genomic region with its contig or chromosome ID
(e.g. NC_000001 or chr1) together with either

a genomic start and end position (9500000 - 1000000)

or a band id (e.g. p35.3 or q41)

Note that the species / genome can be selected via the "Current Genome" option (top right of page).

Select genome(s) to search

Select organism(s)

By default the genome of the currently selected genome (top right on the page) is searched.
Check one or several of the other available organisms if you want to extend
your search to other genomes.

Chip Probes

Display probes from chip

Chip probes from several Affymetrix
microarrays have been mapped onto the corresponding genomes. The mapped
chip probes are displayed in the "Genome Browser", the "Annotation & Analysis" table,
and the
"Alternative Transcripts" output. Per default the newest
chip for each organism is selected.